Calcium in PDB 7mms: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound

Enzymatic activity of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound

All present enzymatic activity of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound, PDB code: 7mms was solved by G.M.Palowitch, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.25 / 1.91
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.354, 104.787, 137.412, 90, 100.29, 90
R / Rfree (%) 20.1 / 22.6

Other elements in 7mms:

The structure of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound (pdb code 7mms). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound, PDB code: 7mms:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7mms

Go back to Calcium Binding Sites List in 7mms
Calcium binding site 1 out of 3 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:40.9
occ:1.00
 OE2 A:GLU52 2.5 30.4 1.0
O B:HOH558 2.7 17.2 1.0
OE1 A:GLU52 2.8 30.0 1.0
CD A:GLU52 3.0 30.0 1.0
NE1 B:TRP41 3.3 11.7 1.0
O B:HOH525 3.3 17.9 1.0
NE A:ARG121 3.5 12.6 1.0
CD A:ARG121 3.7 12.5 1.0
CD A:PRO51 4.0 18.0 1.0
CD1 B:TRP41 4.2 11.6 1.0
CE2 B:TRP41 4.2 11.7 1.0
CG A:PRO51 4.2 18.3 1.0
CD2 A:LEU50 4.3 14.4 1.0
CB A:LEU50 4.3 14.7 1.0
CG A:GLU52 4.4 29.3 1.0
CZ2 B:TRP41 4.4 11.6 1.0
OD1 B:ASN42 4.5 13.9 1.0
CG A:LEU50 4.7 14.6 1.0
CZ A:ARG121 4.7 12.6 1.0
OG1 B:THR45 4.7 12.0 1.0
CD1 A:LEU50 4.7 14.6 1.0
CG A:ARG121 4.7 12.5 1.0
N A:PRO51 4.9 17.5 1.0

Calcium binding site 2 out of 3 in 7mms

Go back to Calcium Binding Sites List in 7mms
Calcium binding site 2 out of 3 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:42.2
occ:1.00
 OE1 B:GLU52 2.4 30.7 1.0
O A:HOH560 2.8 16.8 1.0
CD B:GLU52 3.0 31.0 1.0
OE2 B:GLU52 3.0 31.2 1.0
O A:HOH547 3.3 18.2 1.0
NE1 A:TRP41 3.3 11.9 1.0
NE B:ARG121 3.4 13.6 1.0
CD B:ARG121 3.5 13.6 1.0
CD B:PRO51 4.1 18.6 1.0
CD1 A:TRP41 4.2 11.9 1.0
CG B:PRO51 4.2 19.1 1.0
CD2 B:LEU50 4.2 15.4 1.0
CE2 A:TRP41 4.2 11.8 1.0
CG B:GLU52 4.3 30.5 1.0
CB B:LEU50 4.4 15.4 1.0
CZ2 A:TRP41 4.5 11.9 1.0
CZ B:ARG121 4.6 13.7 1.0
OD1 A:ASN42 4.6 14.4 1.0
CG B:ARG121 4.6 13.6 1.0
CG B:LEU50 4.6 15.5 1.0
CD1 B:LEU50 4.7 15.7 1.0
OG1 A:THR45 4.7 12.4 1.0
N B:PRO51 4.9 18.3 1.0
NH2 B:ARG121 4.9 13.7 1.0

Calcium binding site 3 out of 3 in 7mms

Go back to Calcium Binding Sites List in 7mms
Calcium binding site 3 out of 3 in the Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Class Ie Ribonucleotide Reductase Beta-Nrdi Complex From Aerococcus Urinae in Semiquinone Form with Cu(I) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca404

b:44.0
occ:1.00
 O C:GLY263 2.3 26.9 1.0
OD1 C:ASP266 2.7 29.9 1.0
OE2 C:GLU267 2.8 27.4 1.0
OE1 C:GLU267 2.8 26.0 1.0
OD2 C:ASP266 3.1 30.8 1.0
CD C:GLU267 3.2 26.3 1.0
CG C:ASP266 3.3 28.3 1.0
C C:GLY263 3.5 25.9 1.0
CA C:GLY263 4.2 25.5 1.0
O C:HOH528 4.4 31.4 1.0
N C:LEU264 4.5 25.6 1.0
CG C:GLU267 4.7 25.2 1.0
CA C:LEU264 4.7 25.0 1.0
CB C:ASP266 4.7 26.6 1.0

Reference:

G.M.Palowitch, A.K.Boal. Ribonucleotide Reductase To Be Published.
Page generated: Fri Jul 19 02:04:54 2024

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